[gmx-users] umbrella sampling using pull codes

mjyang mjyang at hku.hk
Thu Sep 12 15:55:48 CEST 2013

Dear GMX users,

   I'd like to perform the umbrella sampling using the pull codes in gromacs. The reaction coordinate is defined as the distance between the center of mass (DCOM) of two domains in a protein. The following script is used:
------------------- only for pull section
; Pull code
pull            = umbrella
pull_geometry   = distance
pull_dim        = N N Y
pull_start      = no
pull_ngroups    = 1
pull_group0     = NN1 ; contained in index file 
pull_group1     = NN2 ; contained in index file 
pull_init1      = 2.5
pull_rate1      = 0.0
pull_k1         = 20000      ; kJ mol^-1 nm^-2
pull_nstxout    = 5000      ; every 2 ps
pull_nstfout    = 5000      ; every 2 ps

I have two questions about the output of gromacs:
1. How is the energy term "COM Pull En." in *.log file calculated? Is it computed as 1/2*kf*(DCOM_t -  pull_init1)^2 at time t?
2. Where is the output information for the evolution of DCOM? Is it in the file pullx.xvg?

Many thanks.


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